Software | Name | Version | Classification |
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SBC-Collect | | data collectionSHELXD | | phasingMLPHARE | | phasingDM | | model buildingARP | | model buildingWARP | | model buildingHKL-3000 | | phasingPHENIX | (phenix.refine: 1.6.4_486)refinementHKL-3000 | | data reductionHKL-3000 | | data scalingDM | | phasing | | | | | | | | | | | |
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Refinement | Method to determine structure: SAD / Resolution: 1.899→45.247 Å / SU ML: 0.2 / σ(F): 0 / σ(I): 0 / Phase error: 15.68 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.1713 | 2646 | 5.09 % | random |
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Rwork | 0.1557 | - | - | - |
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all | 0.1565 | 51937 | - | - |
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obs | 0.1565 | 51937 | 97.83 % | - |
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.309 Å2 / ksol: 0.354 e/Å3 |
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Displacement parameters | | Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 0.452 Å2 | 0 Å2 | -0 Å2 |
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2- | - | 0.452 Å2 | 0 Å2 |
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3- | - | - | -0.904 Å2 |
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Refinement step | Cycle: LAST / Resolution: 1.899→45.247 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 3104 | 0 | 29 | 341 | 3474 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.007 | 3248 | X-RAY DIFFRACTION | f_angle_d0.944 | 4400 | X-RAY DIFFRACTION | f_dihedral_angle_d14.661 | 1178 | X-RAY DIFFRACTION | f_chiral_restr0.068 | 458 | X-RAY DIFFRACTION | f_plane_restr0.004 | 569 | | | | | |
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LS refinement shell | Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Refine-ID | % reflection obs (%) |
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1.8985-1.9664 | 0.2474 | 244 | 0.21 | 4546 | X-RAY DIFFRACTION | 91 | 1.9664-2.0451 | 0.2164 | 267 | 0.1744 | 4723 | X-RAY DIFFRACTION | 95 | 2.0451-2.1382 | 0.1801 | 254 | 0.1478 | 4814 | X-RAY DIFFRACTION | 97 | 2.1382-2.2509 | 0.1704 | 284 | 0.1434 | 4872 | X-RAY DIFFRACTION | 98 | 2.2509-2.392 | 0.1827 | 265 | 0.1478 | 4951 | X-RAY DIFFRACTION | 99 | 2.392-2.5766 | 0.1736 | 247 | 0.157 | 4996 | X-RAY DIFFRACTION | 99 | 2.5766-2.8359 | 0.1818 | 274 | 0.1695 | 5005 | X-RAY DIFFRACTION | 100 | 2.8359-3.2461 | 0.1918 | 261 | 0.1763 | 5062 | X-RAY DIFFRACTION | 100 | 3.2461-4.0894 | 0.1535 | 287 | 0.1491 | 5069 | X-RAY DIFFRACTION | 100 | 4.0894-45.2603 | 0.1527 | 263 | 0.1426 | 5253 | X-RAY DIFFRACTION | 99 |
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Refinement TLS params. | Method: refined / Origin x: 74.1959 Å / Origin y: 39.2468 Å / Origin z: 42.9306 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | 0.2411 Å2 | 0.0031 Å2 | -0.0434 Å2 | - | 0.1488 Å2 | -0.084 Å2 | - | - | 0.1974 Å2 |
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L | 0.6735 °2 | 0.1514 °2 | -0.1423 °2 | - | 0.379 °2 | -0.0151 °2 | - | - | 0.3986 °2 |
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S | -0.0024 Å ° | 0.1285 Å ° | -0.1832 Å ° | -0.0847 Å ° | 0.0435 Å ° | -0.0225 Å ° | 0.1977 Å ° | -0.0189 Å ° | -0.0334 Å ° |
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Refinement TLS group | Selection details: chain A |
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